Phase Space Invaders (ψ)
With the convergence of data, computing power, and new methods, computational biology is at its most exciting moment. At PSI, we're asking the leading researchers in the field to discover where we're headed for, and which exciting pathways will take us there. Whether you're just thinking of starting your research career or have been computing stuff for decades, come and join the conversation!
Episodes
33 episodes
Episode 29 - Jérôme Hénin: Free energy methods, building useful software, and human learning from biomolecular systems
Jerome starts our conversation by reviewing the history of the ABF method and its advantages compared to the main competitors, and connects it to the development of COLVARS, historically very parallel to how the development of the Plumed tool s...
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Season 4
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Episode 29
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46:01
Episode 28 - Yuji Sugita: Replica exchange, software for massive simulations, and importance of long-distance collaborations
In Episode 28, Yuji Sugita shares the story of how he developed temperature replica exchange in the lab of Yuko Okamoto, connecting to his early experience from working with Nobuhiro Go, the father of Go models. We then talk about the process o...
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Season 4
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Episode 28
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38:54
Episode 27 - Kresten Lindorff-Larsen: Refining force fields, the science of intrinsically disordered proteins, and writing better grant proposals
In episode 27, Kresten starts by explaining his path from a wet lab biochemist to a computational biophysicist, a story full of open-ended explorations and helpful mentors. He gives us some background on how both the legacy and latest models de...
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Season 4
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Episode 27
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49:42
Episode 26 - Pratyush Tiwary: Infusing AI with physics, understanding emergent phenomena, the value of education and thinking
In episode 26, we talk about the origins of Pratyush's passion for statistical mechanics, deeply rooted in his background in material science, and think about how we can promote a profound understanding of statmech theory among people working i...
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Season 4
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Episode 26
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44:16
Episode 25 - Ivet Bahar: Elastic network models, targeting hinges for drug discovery, persistence and alertness
In episode 25, Ivet and me start with a general overview of the elastic network theory and its applications to biology, as well as its strengths and limitations. Ivet then tells us about the specific takeaways from the different lines of her re...
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Season 4
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Episode 25
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39:32
Episode 24 - Katarzyna Marcinkiewicz [Nature Communications]: The job of a full-time editor, transparency and other novelties in publishing, and coaching the review process
In episode 24, Katarzyna talks about the everyday concerns and common threads of an editor's job, from continuously learning about the rapid developments in the field to navigating the review process. She shares some inside stories about the ex...
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Season 3
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Episode 24
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49:16
Episode 23 - Zoe Cournia: Precision medicine, designing allosteric drugs, and the role of an academic editor
In episode 23, Zoe and me discuss the current status and promises of drug design, a field where many things seem trivial but nothing is really simple. Zoe talks about the challenges that precision medicine is facing, and how it fits into the gr...
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Season 3
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Episode 23
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50:00
Episode 22 - Lucie Delemotte: Enhanced sampling methods, alternative publishing models, and becoming a parent in academia
In episode 22, we start by talking about the 2022 review of enhanced sampling methods that Lucie co-authored, one that provides long-needed organizing principles and unifying vocabulary for applications in this field. We also outline some chall...
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Season 3
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Episode 22
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48:58
Episode 21 - Tamar Schlick: A mathematician's path to biology, RNA frameshifting, and why scientists (should!) run
In episode 21, Tamar first explains how her unique background impacted the way she approached and conceptualized problems in biology, and how her research projects were born in the first place. We talk about the more recent research coming from...
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Season 3
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Episode 21
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44:49
Episode 20 - Rommie Amaro: Simulating viruses, cross-disciplinary complexity, and the brain drain
In episode 20, I start by asking Rommie how their research on the SARS-CoV-2 virus first unfolded during the early days of the pandemic, and from this story, we move on to discuss her original motivation to study large complex systems. We touch...
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Season 3
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Episode 20
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42:52
Episode 19 - Alex MacKerell: Simple physics, missing experimental data, and model compatibility
In episode 19, Alex and I discuss the history and future of developments in the CHARMM family of force fields, and whether Alex believes there is more physics that we need to include in our classical energy functions to work around our current ...
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Season 3
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Episode 19
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26:14
Episode 18 - Erik Lindahl: Finding simple and novel ideas, starting an experimental lab, and ligand-gated ion channels
In Episode 18, Erik Lindahl reminds us that despite our dependence on computational power and advanced technology, real breakthroughs are often waiting for those who have the patience to think carefully, come up with eye-opening ideas, and foll...
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Season 3
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Episode 18
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36:58
Episode 17 - Caroline Lynn Kamerlin: Deep interdisciplinarity, enzyme promiscuity, and science in society
In episode seventeen, Caroline Lynn Kamerlin talks about the art of asking bold and impactful scientific questions, as well as how to engage in truly interdisciplinary research, something she sees as a consequence of her formal background in na...
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Season 3
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Episode 17
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40:30
Episode 16 - Janusz Bujnicki: Structural modeling, RNA modifications, and advising policy-makers on science
In the sixteenth episode, Janusz Bujnicki tells me about his early switch to bioinformatics, a stroke of serendipity that defined his future career, and how he later managed to reincorporate both biophysics and experimental biology into his res...
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Season 2
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Episode 16
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28:51
Episode 15 - Paulo CT Souza: Developing a universal coarse-grained force field, and approaching the science of molecular complexity
In the fifteenth episode, Paulo Souza and I discuss the challenges inherent in managing a project of such a scope, and the philosophy behind the systematic way in which Martini is continuously improved and reparameterized. Paulo describes how a...
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Season 2
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Episode 15
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26:41
Episode 14 - Syma Khalid: New ways to fight bacteria, the bacterial envelope, and kindness & openness in academia
In the fourteenth episode, Syma Khalid and I talk about the challenges we're faced with when trying to understand the environment of the bacterial cell envelope, and the outer membrane in particular. We discuss how the lessons taken from the co...
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Season 2
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Episode 14
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23:00
Episode 13 - Daniel Zuckerman: Trajectory ensembles, writing books, and learning biology through physics
In the thirteenth episode, Daniel Zuckerman and I talk about textbooks on statistical biophysics and a physics-based vision of biology, a few of which he himself authored. Daniel reveals that his passion for clarity in writing comes from his ea...
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Season 2
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Episode 13
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29:45
Episode 12 - Vlad Cojocaru: Simulating transcriptional regulation, returning to our home countries, and the scales of the genome
In the twelfth episode, Vlad Cojocaru and I discuss how the simulation field can integrate further layers of complexity in modeling transcription control and genome organization in humans. Vlad shares his insights on the computational biology o...
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Season 2
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Episode 12
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27:12
Episode 11 - Justin Lemkul: Providing technical help online, sharing expertise, and polarization in nucleic acids
In the eleventh episode, Justin Lemkul and I talk about the motivations and challenges behind providing technical help on online forums and mailing lists. Justin shares his story of becoming a prolific technical advisor for the Gromacs communit...
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Season 2
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Episode 11
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29:38
Episode 10 - Ariane Nunes-Alves: Kinetics in drug design, molecular crowding, and the social life of a PI
In the tenth episode, Ariane Nunes-Alves and I talk about a kinetics-centric view of drug design, making the case that modeling kinetics in atomistic simulation is an important frontier that, despite clear biomedical relevance, is rarely explic...
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Season 2
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Episode 10
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19:13
Episode 9 - Michele Vendruscolo: Preventing protein misfolding, fostering public engagement of scientists, and AI tools in drug design
In the ninth episode, Michele Vendruscolo and I discuss the current state of research on misfolding diseases, typically associated with excessive protein aggregation and formation of insoluble amyloids. Michele presents an optimistic perspectiv...
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Season 2
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Episode 9
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31:21
Episode 8½ - My commentary: Wrapping up the first season
In this episode, I'm attempting to string together the most common threads brought up by my guests in the first eight interviews on the podcast. Reflecting on these conversations, I'm suggesting some grand challenges for the field in the years ...
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Season 1
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Episode 8
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20:15
Episode 8 - Rossen Apostolov [BioExcel]: Managing scientific collaboration, the biggest project of European biophysics, and seeding schools of thought
In the eight episode, Rossen Apostolov and I depart from the standard format to talk about the core concepts behind BioExcel, the European Center of Excellence for computational biology. We discuss their main objectives and challenges, from wor...
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Season 1
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Episode 8
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27:13